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Detailed information for vg0427290211:

Variant ID: vg0427290211 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27290211
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

TCATCTTCCTCCTCACCTTCATCTTCCCCTTCTCCGTCCCCTTCCACCTGCCCATCAGTCAATCTGGCCTATTATTACCTCATCAAACCCTAATCAACAG[G/A]
AGGCTACAACCTCAATTCAAGGTGTTAGCTAGGACGAGGTGATCGATCATCGTACTCACCATGAATTAGGCCCATGGCAAGTGGTTGCGGTGGCAGCTGC

Reverse complement sequence

GCAGCTGCCACCGCAACCACTTGCCATGGGCCTAATTCATGGTGAGTACGATGATCGATCACCTCGTCCTAGCTAACACCTTGAATTGAGGTTGTAGCCT[C/T]
CTGTTGATTAGGGTTTGATGAGGTAATAATAGGCCAGATTGACTGATGGGCAGGTGGAAGGGGACGGAGAAGGGGAAGATGAAGGTGAGGAGGAAGATGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.50%	28.90%	0.59%	0.00%	NA
All Indica	2759	94.20%	5.50%	0.36%	0.00%	NA
All Japonica	1512	22.20%	76.60%	1.19%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	91.90%	7.10%	1.01%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	93.20%	6.70%	0.11%	0.00%	NA
Indica Intermediate	786	93.80%	5.90%	0.38%	0.00%	NA
Temperate Japonica	767	5.00%	94.40%	0.65%	0.00%	NA
Tropical Japonica	504	46.00%	51.80%	2.18%	0.00%	NA
Japonica Intermediate	241	27.40%	71.80%	0.83%	0.00%	NA
VI/Aromatic	96	68.80%	31.20%	0.00%	0.00%	NA
Intermediate	90	71.10%	28.90%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0427290211	G -> A	LOC_Os04g46060.1	intron_variant ; MODIFIER	silent_mutation	Average:62.813; most accessible tissue: Callus, score: 76.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427290211	NA	9.53E-13	mr1641	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	1.80E-18	mr1653	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	4.56E-06	mr1653	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	8.10E-08	mr1659	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	5.44E-18	mr1767	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	1.09E-12	mr1853	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	1.28E-13	mr1909	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0427290211	NA	2.43E-10	mr1921	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251